X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=d7a8f001c5f34599ebaf0dfbb06d22e9d1c0c20e;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=959c83c28264a1a1bc73219b2d3958a0e4483cf2;hpb=c3162a6dd5f226c743bce629cf125a17c9b67711;p=jalview.git

diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java
index 959c83c..d7a8f00 100755
--- a/src/jalview/gui/IdCanvas.java
+++ b/src/jalview/gui/IdCanvas.java
@@ -1,176 +1,513 @@
-package jalview.gui;
-
-import java.awt.*;
-import java.awt.Graphics2D.*;
-import java.awt.image.*;
-import javax.swing.*;
-import jalview.datamodel.*;
-import jalview.analysis.*;
-public class IdCanvas extends JPanel
-{
-  protected AlignViewport av;
-
-  protected boolean showScores  = true;
-
-  protected int     maxIdLength = -1;
-  protected String  maxIdStr    = null;
-  BufferedImage image;
-  Graphics2D gg;
-  int imgHeight=0;
-  boolean fastPaint = false;
-
-  public IdCanvas(AlignViewport av)
-  {
-    setLayout(new BorderLayout());
-    this.av         = av;
-    PaintRefresher.Register(this);
-  }
-
-  public void drawIdString(Graphics2D gg,SequenceI s,int i, int starty, int ypos) {
-      int charHeight = av.getCharHeight();
-
-
-      if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(s)) {
-	  gg.setColor(Color.lightGray);
-	  gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),charHeight);
-	  gg.setColor(Color.white);
-      } else {
-	  gg.setColor(s.getColor());
-	  gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),charHeight);
-	  gg.setColor(Color.black);
-      }
-
-      String string = s.getName();
-      if(av.getShowFullId())
-        string = s.getDisplayId();
-
-      gg.drawString(string,0,AlignmentUtil.getPixelHeight(starty,i,charHeight) + ypos + charHeight-   (charHeight/5));
-
-  }
-
-  public void fastPaint(int vertical)
-  {
-    if(gg==null)
-    {  repaint(); return;}
-
-    gg.copyArea( 0,0, getWidth(), imgHeight, 0, -vertical*av.charHeight );
-
-    int ss=av.startSeq, es=av.endSeq, transY = 0;
-     if(vertical>0)    // scroll down
-     {
-       transY = imgHeight - vertical*av.charHeight;
-       ss = es - vertical;
-     }
-     else if(vertical<0)
-     {
-       es = ss-vertical;
-     }
-
-        gg.translate(0, transY);
-
-        drawIds(ss, es);
-
-        gg.translate( 0, -transY );
-
-
-      fastPaint = true;
-      repaint();
-  }
-
-  public void paintComponent(Graphics g)
-  {
-    g.setColor(Color.white);
-    g.fillRect(0, 0, getWidth(), getHeight());
-
-    if (fastPaint)
-    {
-      g.drawImage(image, 0, 0, this);
-      fastPaint = false;
-      return;
-    }
-
-    imgHeight = getHeight();
-    imgHeight -= imgHeight % av.charHeight;
-    image = new BufferedImage(getWidth(), imgHeight, BufferedImage.TYPE_INT_RGB);
-    gg = (Graphics2D) image.getGraphics();
-    //Fill in the background
-    gg.setColor(Color.white);
-    gg.fillRect(0, 0, getWidth(), imgHeight);
-    gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
-                        RenderingHints.VALUE_ANTIALIAS_ON);
-    Font italic = new Font(av.getFont().getName(), Font.ITALIC,
-                           av.getFont().getSize());
-    gg.setFont(italic);
-
-    drawIds( av.getStartSeq(), av.endSeq);
-
-    g.drawImage(image, 0, 0, this);
-  }
-
-  void drawIds(int starty, int endy)
-  {
-
-    Color currentColor     = Color.white;
-    Color currentTextColor = Color.black;
-
-    if (av.getWrapAlignment())
-    {
-          // Draw the rest of the panels
-          int chunkHeight =  (av.alignment.getHeight() + 2)*av.charHeight;
-          int row = av.getStartRes() / av.chunkWidth ;
-          for(int ypos=2*av.charHeight;
-              ypos <= getHeight() && row*av.chunkWidth<av.alignment.getWidth();
-              ypos += chunkHeight, row++ )
-          {
-            for (int i = starty; i < av.alignment.getHeight(); i++)
-            {
-              SequenceI s = av.alignment.getSequenceAt(i);
-              drawIdString(gg, s, i, 0, ypos);
-            }
-          }
-
-
-    } else
-    {
-
-      //Now draw the id strings
-      for (int i = starty; i < endy; i++)
-      {
-        // Selected sequence colours
-
-        if (av.getSelectionGroup()!= null
-            && av.getSelectionGroup().sequences.contains(av.alignment.getSequenceAt(i)))
-        {
-       //   if(av.alignment.findGroup(al.getSequenceAt(i)).getEndRes()==
-          currentColor = Color.lightGray;
-          currentTextColor = Color.black;
-        }
-        else
-        {
-          currentColor = av.alignment.getSequenceAt(i).getColor();
-          currentTextColor = Color.black;
-        }
-
-        gg.setColor(currentColor);
-
-        gg.fillRect(0,
-                    AlignmentUtil.getPixelHeight(starty, i, av.charHeight),
-                    getWidth(),
-                    av.charHeight);
-
-        gg.setColor(currentTextColor);
-        String string = av.alignment.getSequenceAt(i).getName();
-        if(av.getShowFullId())
-          string = av.alignment.getSequenceAt(i).getDisplayId();
-        gg.drawString(string, 0,
-                      AlignmentUtil.getPixelHeight(starty, i, av.charHeight) +
-                      av.charHeight - (av.charHeight / 5));
-      }
-
-      // add a border
-      gg.setColor(Color.white);
-      gg.fillRect(getWidth()-4,0,4,getHeight());
-    }
-
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.datamodel.SequenceI;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.image.BufferedImage;
+import java.util.List;
+
+import javax.swing.JPanel;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdCanvas extends JPanel
+{
+  protected AlignViewport av;
+
+  protected boolean showScores = true;
+
+  protected int maxIdLength = -1;
+
+  protected String maxIdStr = null;
+
+  BufferedImage image;
+
+  Graphics2D gg;
+
+  int imgHeight = 0;
+
+  boolean fastPaint = false;
+
+  List<SequenceI> searchResults;
+
+  FontMetrics fm;
+
+  AnnotationLabels labels = null;
+
+  AnnotationPanel ap;
+
+  private Font idfont;
+
+  /**
+   * Creates a new IdCanvas object.
+   * 
+   * @param av
+   *          DOCUMENT ME!
+   */
+  public IdCanvas(AlignViewport av)
+  {
+    setLayout(new BorderLayout());
+    this.av = av;
+    PaintRefresher.Register(this, av.getSequenceSetId());
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param gg
+   *          DOCUMENT ME!
+   * @param hiddenRows
+   *          true - check and display hidden row marker if need be
+   * @param s
+   *          DOCUMENT ME!
+   * @param i
+   *          DOCUMENT ME!
+   * @param starty
+   *          DOCUMENT ME!
+   * @param ypos
+   *          DOCUMENT ME!
+   */
+  public void drawIdString(Graphics2D gg, boolean hiddenRows, SequenceI s,
+          int i, int starty, int ypos)
+  {
+    int xPos = 0;
+    int panelWidth = getWidth();
+    int charHeight = av.getCharHeight();
+
+    if ((searchResults != null) && searchResults.contains(s))
+    {
+      gg.setColor(Color.black);
+      gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+              charHeight);
+      gg.setColor(Color.white);
+    }
+    else if ((av.getSelectionGroup() != null)
+            && av.getSelectionGroup().getSequences(null).contains(s))
+    {
+      gg.setColor(Color.lightGray);
+      gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+              charHeight);
+      gg.setColor(Color.white);
+    }
+    else
+    {
+      gg.setColor(av.getSequenceColour(s));
+      gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+              charHeight);
+      gg.setColor(Color.black);
+    }
+
+    if (av.isRightAlignIds())
+    {
+      xPos = panelWidth
+              - fm.stringWidth(s.getDisplayId(av.getShowJVSuffix())) - 4;
+    }
+
+    gg.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos,
+            (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
+
+    if (hiddenRows)
+    {
+      drawMarker(i, starty, ypos);
+    }
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param vertical
+   *          DOCUMENT ME!
+   */
+  public void fastPaint(int vertical)
+  {
+    if (gg == null)
+    {
+      repaint();
+
+      return;
+    }
+
+    gg.copyArea(0, 0, getWidth(), imgHeight, 0,
+            -vertical * av.getCharHeight());
+
+    int ss = av.startSeq;
+    int es = av.endSeq;
+    int transY = 0;
+
+    if (vertical > 0) // scroll down
+    {
+      ss = es - vertical;
+
+      if (ss < av.startSeq)
+      { // ie scrolling too fast, more than a page at a time
+        ss = av.startSeq;
+      }
+      else
+      {
+        transY = imgHeight - (vertical * av.getCharHeight());
+      }
+    }
+    else if (vertical < 0)
+    {
+      es = ss - vertical;
+
+      if (es > av.endSeq)
+      {
+        es = av.endSeq;
+      }
+    }
+
+    gg.translate(0, transY);
+
+    drawIds(ss, es);
+
+    gg.translate(0, -transY);
+
+    fastPaint = true;
+    repaint();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param g
+   *          DOCUMENT ME!
+   */
+  public void paintComponent(Graphics g)
+  {
+    g.setColor(Color.white);
+    g.fillRect(0, 0, getWidth(), getHeight());
+
+    if (fastPaint)
+    {
+      fastPaint = false;
+      g.drawImage(image, 0, 0, this);
+
+      return;
+    }
+
+    int oldHeight = imgHeight;
+
+    imgHeight = getHeight();
+    imgHeight -= (imgHeight % av.getCharHeight());
+
+    if (imgHeight < 1)
+    {
+      return;
+    }
+
+    if (oldHeight != imgHeight || image.getWidth(this) != getWidth())
+    {
+      image = new BufferedImage(getWidth(), imgHeight,
+              BufferedImage.TYPE_INT_RGB);
+    }
+
+    gg = (Graphics2D) image.getGraphics();
+
+    // Fill in the background
+    gg.setColor(Color.white);
+    gg.fillRect(0, 0, getWidth(), imgHeight);
+
+    drawIds(av.getStartSeq(), av.endSeq);
+
+    g.drawImage(image, 0, 0, this);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param starty
+   *          DOCUMENT ME!
+   * @param endy
+   *          DOCUMENT ME!
+   */
+  void drawIds(int starty, int endy)
+  {
+    if (av.isSeqNameItalics())
+    {
+      setIdfont(new Font(av.getFont().getName(), Font.ITALIC, av.getFont()
+              .getSize()));
+    }
+    else
+    {
+      setIdfont(av.getFont());
+    }
+
+    gg.setFont(getIdfont());
+    fm = gg.getFontMetrics();
+
+    if (av.antiAlias)
+    {
+      gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+              RenderingHints.VALUE_ANTIALIAS_ON);
+    }
+
+    Color currentColor = Color.white;
+    Color currentTextColor = Color.black;
+
+    final boolean doHiddenCheck = av.isDisplayReferenceSeq()
+            || av.hasHiddenRows(), hiddenRows = av.hasHiddenRows();
+
+    if (av.getWrapAlignment())
+    {
+      int maxwidth = av.getAlignment().getWidth();
+      int alheight = av.getAlignment().getHeight();
+
+      if (av.hasHiddenColumns())
+      {
+        maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+      }
+
+      int annotationHeight = 0;
+
+      if (av.isShowAnnotation())
+      {
+        if (ap == null)
+        {
+          ap = new AnnotationPanel(av);
+        }
+
+        annotationHeight = ap.adjustPanelHeight();
+        if (labels == null)
+        {
+          labels = new AnnotationLabels(av);
+        }
+      }
+
+      int hgap = av.getCharHeight();
+      if (av.getScaleAboveWrapped())
+      {
+        hgap += av.getCharHeight();
+      }
+
+      int cHeight = alheight * av.getCharHeight() + hgap + annotationHeight;
+
+      int rowSize = av.getEndRes() - av.getStartRes();
+
+      // Draw the rest of the panels
+      for (int ypos = hgap, row = av.startRes; (ypos <= getHeight())
+              && (row < maxwidth); ypos += cHeight, row += rowSize)
+      {
+        for (int i = starty; i < alheight; i++)
+        {
+          SequenceI s = av.getAlignment().getSequenceAt(i);
+          if (doHiddenCheck)
+          {
+            setHiddenFont(s);
+          }
+          else
+          {
+            gg.setFont(getIdfont());
+          }
+
+          drawIdString(gg, hiddenRows, s, i, 0, ypos);
+        }
+
+        if (labels != null && av.isShowAnnotation())
+        {
+          gg.translate(0, ypos + (alheight * av.getCharHeight()));
+          labels.drawComponent(gg, getWidth());
+          gg.translate(0, -ypos - (alheight * av.getCharHeight()));
+        }
+      }
+    }
+    else
+    {
+      // No need to hang on to labels if we're not wrapped
+      labels = null;
+
+      // Now draw the id strings
+      int panelWidth = getWidth();
+      int xPos = 0;
+
+      SequenceI sequence;
+      // Now draw the id strings
+      for (int i = starty; i < endy; i++)
+      {
+        sequence = av.getAlignment().getSequenceAt(i);
+
+        if (sequence == null)
+        {
+          continue;
+        }
+
+        if (doHiddenCheck)
+        {
+          setHiddenFont(sequence);
+        }
+
+        // Selected sequence colours
+        if ((searchResults != null) && searchResults.contains(sequence))
+        {
+          currentColor = Color.black;
+          currentTextColor = Color.white;
+        }
+        else if ((av.getSelectionGroup() != null)
+                && av.getSelectionGroup().getSequences(null)
+                        .contains(sequence))
+        {
+          currentColor = Color.lightGray;
+          currentTextColor = Color.black;
+        }
+        else
+        {
+          currentColor = av.getSequenceColour(sequence);
+          currentTextColor = Color.black;
+        }
+
+        gg.setColor(currentColor);
+
+        gg.fillRect(0, (i - starty) * av.getCharHeight(), getWidth(),
+                av.getCharHeight());
+
+        gg.setColor(currentTextColor);
+
+        String string = sequence.getDisplayId(av.getShowJVSuffix());
+
+        if (av.isRightAlignIds())
+        {
+          xPos = panelWidth - fm.stringWidth(string) - 4;
+        }
+
+        gg.drawString(string, xPos,
+                (((i - starty) * av.getCharHeight()) + av.getCharHeight())
+                        - (av.getCharHeight() / 5));
+
+        if (hiddenRows)
+        {
+          drawMarker(i, starty, 0);
+        }
+
+      }
+
+    }
+  }
+
+  void drawMarker(int i, int starty, int yoffset)
+  {
+
+    SequenceI[] hseqs = av.getAlignment().getHiddenSequences().hiddenSequences;
+    // Use this method here instead of calling hiddenSeq adjust
+    // 3 times.
+    int hSize = hseqs.length;
+
+    int hiddenIndex = i;
+    int lastIndex = i - 1;
+    int nextIndex = i + 1;
+
+    for (int j = 0; j < hSize; j++)
+    {
+      if (hseqs[j] != null)
+      {
+        if (j - 1 < hiddenIndex)
+        {
+          hiddenIndex++;
+        }
+        if (j - 1 < lastIndex)
+        {
+          lastIndex++;
+        }
+        if (j - 1 < nextIndex)
+        {
+          nextIndex++;
+        }
+      }
+    }
+
+    boolean below = (hiddenIndex > lastIndex + 1);
+    boolean above = (nextIndex > hiddenIndex + 1);
+
+    gg.setColor(Color.blue);
+    if (below)
+    {
+      gg.fillPolygon(
+              new int[] { getWidth() - av.getCharHeight(),
+                  getWidth() - av.getCharHeight(), getWidth() },
+              new int[] {
+                  (i - starty) * av.getCharHeight() + yoffset,
+                  (i - starty) * av.getCharHeight() + yoffset
+                          + av.getCharHeight() / 4,
+                  (i - starty) * av.getCharHeight() + yoffset }, 3);
+    }
+    if (above)
+    {
+      gg.fillPolygon(
+              new int[] { getWidth() - av.getCharHeight(),
+                  getWidth() - av.getCharHeight(), getWidth() },
+              new int[] {
+                  (i - starty + 1) * av.getCharHeight() + yoffset,
+                  (i - starty + 1) * av.getCharHeight() + yoffset
+                          - av.getCharHeight() / 4,
+                  (i - starty + 1) * av.getCharHeight() + yoffset }, 3);
+
+    }
+  }
+
+  void setHiddenFont(SequenceI seq)
+  {
+    Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
+            .getSize());
+
+    if (av.isHiddenRepSequence(seq))
+    {
+      gg.setFont(bold);
+    }
+    else
+    {
+      gg.setFont(getIdfont());
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param list
+   *          DOCUMENT ME!
+   */
+  public void setHighlighted(List<SequenceI> list)
+  {
+    searchResults = list;
+    repaint();
+  }
+
+  public Font getIdfont()
+  {
+    return idfont;
+  }
+
+  public void setIdfont(Font idfont)
+  {
+    this.idfont = idfont;
+  }
+}